Effects of geological structures on groundwater geochemistry and groundwater flow within deep basement aquifers of Lilongwe, Malawi

Understanding the influence of geological structures on groundwater geochemistry and flow is critical for sustainable water management in basement aquifers, yet data remain limited in Malawi. This study evaluated the role of geological structures in controlling groundwater chemistry and flow within the deep basement aquifers of Lilongwe using a quantitative experimental design. Groundwater samples were collected from 21 deep wells and 50 shallow wells following APHA (2017) and Malawi Standard MS 682 − 11:2012 protocols, with hydrogeological parameters such as borehole yield, water strike depth, and static water level recorded. Lithological data were obtained from rock chips at 1 m intervals and logged using Rockworks 17, while spatial maps were prepared in ArcGIS v10.5 using the Inverse Distance Weighted (IDW) method. Lineaments were delineated using LANDSAT ETM imagery processed in PCI Geomatica, and statistical analysis was conducted in IBM SPSS 25.0 with Principal Component Analysis (PCA). Results revealed five principal components explaining 80.31% of the variance: PC1 (38.4%) showed strong positive loadings in EC, TDS (ranging from < 1000 mg/L in recharge zones to > 2500 mg/L in fault-influenced zones), HCO₃⁻, Cl⁻, SO₄²⁻, Na⁺, Ca²⁺, and Mg²⁺, reflecting dissolution from rock–water interactions; PC2 (14.3%) indicated deep-seated fault influence through positive SO₄²⁻ and negative Cd²⁺ loadings; PC3 (11%) highlighted Fe²⁺ and Mn²⁺ linked to evaporation and regional flow; PC4 (10%) showed carbonate dissolution (CO₃²⁻, pH); and PC5 (6.66%) reflected minor water–rock interactions via F⁻. Hydrochemical facies included Ca-HCO₃, Ca + Mg-SO₄, Na + K-HCO₃, and Ca-SO₄ types, with Ca-HCO₃ dominant, consistent with active recharge and low TDS. Spatially, Ca-SO₄ and Ca-Mg-SO₄ types were confined to central and northern zones, Na + K-HCO₃ occurred in northern and southern zones, and Ca-HCO₃ varied along SE–NW trending faults. Groundwater flow systems were classified as local (weathered zone), intermediate (weathered and fractured zones), and regional (deep fractured aquifers), with fractures controlling recharge and flow pathways. Overall, the findings demonstrate that geological structures significantly influence groundwater geochemistry and flow, providing essential insights for policymakers to design sustainable groundwater abstraction and management strategies in Malawi’s basement aquifers.